UTR-Diffusion: Conditional Diffusion Modeling for Multi-objective and Constrained UTR Design

Abstract

Motivation The 5′ untranslated region (UTR) and the start-codon-proximal region of the coding sequence (CDS) jointly influence translation efficiency and local RNA secondary-structure stability, while synonymous codon choices throughout the CDS shape codon adaptation. Because the encoded protein is often predetermined, practical mRNA design must coordinate these quantitative objectives while preserving specified nucleotide sequences and amino-acid identities. Existing generative approaches typically address continuous-valued targeting, explicit sequence constraints, and codon-usage control separately rather than integrating all three within a single model. Results We present UTR-Diffusion, a diffusion-based framework for 5′ UTR and 5′ UTR–CDS junction design. UTR-Diffusion conditions generation on continuous-valued MRL and MFE targets and supports nucleotide-level constraints, amino-acid-level constraints with synonymous-codon flexibility, and codon-adaptiveness control that modulates the sequence-level codon adaptation index (CAI). Systematic evaluations across dense MRL–MFE target grids showed that generated distributions shifted consistently with both targets, retained substantial diversity, and strictly preserved specified nucleotide sequences and amino-acid identities. Codon-adaptiveness control yielded distinct, monotonically ordered CAI levels that closely followed the specified adaptiveness targets. In comparative benchmarks, UTR-Diffusion outperformed representative existing methods in high-MRL optimization and precise MRL targeting for 5′ UTR design, and achieved higher MRL, less-negative junction MFE, and higher CAI than peptide-preserving baselines in 50-nt 5′ UTR–CDS junction design. Availability Implementation and trained models for UTR-Diffusion are available at https://github.com/sato-lab-org/utr-diffusion. Supplementary information Supplementary data are available with the preprint